The Encoder library has not had support for the ATmega4809 microcontroller of the Nano Every added yet.
Since all the microcontroller-specific code in the library is for interrupts, the workaround should be to use the "ENCODER_DO_NOT_USE_INTERRUPTS" mode of the library, as demonstrated in the library's NoInterrupts example.
However, there seems to be a bug in the Encoder library when used in this mode. I believe I have a fix for the bug:
Open /Users/eraxeg/Documents/Arduino/libraries/Encoder/Encoder.cpp in a text editor.
Add the following line to the very top of the file:
#define FROM_ENCODER_CPP
Save the file.
Open /Users/eraxeg/Documents/Arduino/libraries/Encoder/Encoder.h in a text editor.
Change line 43 from:
#if defined(ENCODER_USE_INTERRUPTS) || !defined(ENCODER_DO_NOT_USE_INTERRUPTS)
to:
#if defined(ENCODER_USE_INTERRUPTS) || (!defined(ENCODER_DO_NOT_USE_INTERRUPTS) && !defined(FROM_ENCODER_CPP))
Save the file.
After that, you should be able to use the library with your Nano Every when in "ENCODER_DO_NOT_USE_INTERRUPTS" mode. Make sure to carefully read and understand the comments at the top of the NoInterrupts example.